Added Slice Collector

This post-fusion processor reads in all the slices of the output directory
and writes them as a stack named 'collected-results.tif' in the data
directory. Just for convenience.

Signed-off-by: Luke Stuyvenberg <[email protected]>

Author: stuyvenberg

src/main/java/org/openspim/toolkit/OpenSPIMToolkit.java

@@ -305,6 +305,10 @@ public static List<Vector3D> loadBeadsSimple(File viewpath) {
 	public static File getRegistrationDirectory(File viewpath) {
 		return new File(viewpath.getParent(), "registration");
 	}
+	
+	public static File getOutputDirectory(File viewpath) {
+		return new File(viewpath.getParent(), "output");
+	}
 
 	public static List<String> readAllLines(File path) throws IOException {
 		List<String> out = new LinkedList<String>();

src/main/java/org/openspim/toolkit/SliceCollector.java

@@ -0,0 +1,96 @@
+package org.openspim.toolkit;
+
+import ij.IJ;
+import ij.ImagePlus;
+import ij.ImageStack;
+
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.Arrays;
+import java.util.concurrent.ExecutionException;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JFileChooser;
+import javax.swing.JTextField;
+import javax.swing.filechooser.FileNameExtensionFilter;
+
+import org.openspim.gui.LayoutUtils;
+
+public class SliceCollector implements Processor {
+	@Override
+	public int getCapabilities() {
+		return Processor.POST_FUSION;
+	}
+
+	@Override
+	public void performProcessing(Params params) throws InterruptedException, ExecutionException {
+		File exemplar = params.spec.iterator().next();
+		File[] files = OpenSPIMToolkit.getOutputDirectory(exemplar).listFiles(tifFilter);
+		Arrays.sort(files);
+
+		ImageStack stack = null;
+
+		for (File f : files) {
+			ImagePlus imp = IJ.openImage(f.getAbsolutePath());
+
+			if(stack == null)
+				stack = new ImageStack(imp.getWidth(), imp.getHeight());
+
+			stack.addSlice(imp.getProcessor());
+			imp.close();
+		}
+
+		ImagePlus total = new ImagePlus("collected-output", stack);
+		if(!pathBox.getText().isEmpty())
+			IJ.saveAsTiff(total, pathBox.getText());
+
+		if(show.isSelected())
+			total.show();
+		else
+			total.close();
+	}
+
+	@Override
+	public String toString() {
+		return "Slice Collector";
+	}
+
+	private static FilenameFilter tifFilter = new FilenameFilter() {
+		@Override
+		public boolean accept(File dir, String name) {
+			return name.endsWith(".tif") || name.endsWith(".tiff");
+		}
+	};
+
+	private static JTextField pathBox = new JTextField("collected-output.tif", 24);
+	private static JButton browseBtn = new JButton("Browse");
+	private static JFileChooser chooser = new JFileChooser();
+	private static JCheckBox show = new JCheckBox();
+
+	static {
+		chooser.addChoosableFileFilter(new FileNameExtensionFilter("Tagged Image File Format", "tif", "tiff"));
+		chooser.setAcceptAllFileFilterUsed(true);
+
+		browseBtn.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent ae) {
+				if(chooser.showSaveDialog(browseBtn) != JFileChooser.APPROVE_OPTION)
+					return;
+
+				pathBox.setText(chooser.getSelectedFile().getAbsolutePath());
+			}
+		});
+	}
+
+	@Override
+	public Component getControlPanel() {
+		return LayoutUtils.form(
+			"Save Path:", LayoutUtils.horizPanel(pathBox, browseBtn),
+			"Show Final Image:", show
+		);
+	}
+}

src/main/resources/META-INF/services/org.openspim.toolkit.Processor

@@ -2,5 +2,6 @@ org.openspim.toolkit.preprocess.OmeMetadataStripper
 org.openspim.toolkit.beadremoval.BeadBlotter
 org.openspim.toolkit.TriViewMultiProcessor$SampleExcluder
 org.openspim.toolkit.TriViewMultiProcessor$SampleIsolator
+org.openspim.toolkit.SliceCollector
 org.openspim.toolkit.adapters.DefaultSPIMRegistration
 org.openspim.toolkit.adapters.DefaultSPIMFusion